tbuckley/cabot-search huggingface dataset:
Screening and Testing for Hepatitis B Virus Infection: CDC Recommendations — United States, 2023
Authors: Erin E. Conners, Lakshmi Panagiotakopoulos, Megan G. Hofmeister, Philip R. Spradling, Liesl M. Hagan, Aaron M. Harris, Jessica S. Rogers-Brown, Carolyn Wester, Noele P. Nelson, Karina Rapposelli, Amy L. Sandul, Elisa Choi, Carla Coffin, Kristen Marks, David L. Thomas, Su H. Wang
Journal: MMWR Recommendations and Reports (2023)

Chronic hepatitis B virus (HBV) infection can lead to substantial morbidity and mortality. Although treatment is not considered curative, antiviral treatment, monitoring, and liver cancer surveillance can reduce morbidity and mortality. Effective vaccines to prevent hepatitis B are available. This report updates and expands CDC's previously published Recommendations for Identification and Public Health Management of Persons with Chronic Hepatitis B Virus Infection (MMWR Recomm Rep 2008;57[No. RR-8]) regarding screening for HBV infection in the United States. New recommendations include hepatitis B screening using three laboratory tests at least once during a lifetime for adults aged ≥18 years. The report also expands risk-based testing recommendations to include the following populations, activities, exposures, or conditions associated with increased risk for HBV infection: persons incarcerated or formerly incarcerated in a jail, prison, or other detention setting; persons with a history of sexually transmitted infections or multiple sex partners; and persons with a history of hepatitis C virus infection. In addition, to provide increased access to testing, anyone who requests HBV testing should receive it, regardless of disclosure of risk, because many persons might be reluctant to disclose stigmatizing risks.
Molecular surveillance reveals the emergence and dissemination of NDM-5-producing Escherichia coli high-risk clones in Germany, 2013 to 2019
Authors: Jörg B Hans, Niels Pfennigwerth, Bernd Neumann, Yvonne Pfeifer, Martin A Fischer, Jessica Eisfeld, Jennifer Schauer, Sebastian Haller, Tim Eckmanns, Sören Gatermann, Guido Werner
Journal: Eurosurveillance (2023)

BackgroundCarbapenemase-producing Enterobacterales (CPE) are rapidly increasing worldwide, also in Europe. Although prevalence of CPE in Germany is comparatively low, the National Reference Centre for Multidrug-resistant Gram-negative Bacteria noted annually increasing numbers of NDM-5-producing Escherichia coli isolates.AimAs part of our ongoing surveillance programme, we characterised NDM-5-producing E. coli isolates received between 2013 and 2019 using whole genome sequencing (WGS).MethodsFrom 329 identified NDM-5-producing E. coli, 224 isolates from known geographical locations were subjected to Illumina WGS. Analyses of 222 sequenced isolates included multilocus sequence typing (MLST), core genome (cg)MLST and single-nucleotide polymorphism (SNP)-based analyses.ResultsResults of cgMLST revealed genetically distinct clusters for many of the 43 detected sequence types (ST), of which ST167, ST410, ST405 and ST361 predominated. The SNP-based phylogenetic analyses combined with geographical information identified sporadic cases of nosocomial transmission on a small spatial scale. However, we identified large clusters corresponding to clonal dissemination of ST167, ST410, ST405 and ST361 strains in consecutive years in different regions in Germany.ConclusionOccurrence of NDM-5-producing E. coli rose in Germany, which was to a large extent due to the increased prevalence of isolates belonging to the international high-risk clones ST167, ST410, ST405 and ST361. Of particular concern is the supra-regional dissemination of these epidemic clones. Available information suggest community spread of NDM-5-producing E. coli in Germany, highlighting the importance of epidemiological investigation and an integrated surveillance system in the One Health framework.
Racial and Ethnic Differences in Subjective Cognitive Decline — United States, 2015–2020
Authors: Karen G. Wooten, Lisa C. McGuire, Benjamin S. Olivari, Eva M. J. Jackson, Janet B. Croft
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Subjective cognitive decline (SCD), the self-reported experience of worsening or more frequent memory loss or confusion, might be a symptom of early-stage dementia or future serious cognitive decline such as Alzheimer disease* or a related dementia (ADRD) (1). Established modifiable risk factors for ADRD include high blood pressure, inadequate physical activity, obesity, diabetes, depression, current cigarette smoking, and hearing loss (2). An estimated 6.5 million persons aged ≥65 years in the United States live with Alzheimer disease, the most common dementia (1). This number is projected to double by 2060, with the largest increase among non-Hispanic Black or African American (Black), and Hispanic or Latino (Hispanic) adults (1,3). Using data from the Behavioral Risk Factor Surveillance System (BRFSS), CDC assessed racial and ethnic, select demographic, and geographical differences in SCD prevalence, and prevalence of health care professional conversations among those reporting SCD. The age-adjusted prevalence of SCD during 2015-2020 was 9.6% among adults aged ≥45 years (5.0% of Asian or Pacific Islander [A/PI] adults, 9.3% of non-Hispanic White [White] adults, 10.1% of Black adults, 11.4% of Hispanic adults, and 16.7% of non-Hispanic American Indian or Alaska Native [AI/AN] adults). College education was associated with a lower prevalence of SCD among all racial and ethnic groups. Only 47.3% of adults with SCD reported that they had discussed confusion or memory loss with a health care professional. Discussing changes in cognition with a physician can allow for the identification of potentially treatable conditions, early detection of dementia, promotion of dementia risk reduction behaviors, and establishing a treatment or care plan to help adults remain healthy and independent for as long as possible.
Immunotherapy Success for Microsatellite Stable Colorectal Cancers—Searching for the Horizon
Authors: Emil Lou
Journal: JAMA Oncology (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
Former NIH Director Francis S. Collins on the New White House Plan to Eliminate Hepatitis C
Authors: Jennifer Abbasi
Journal: JAMA (2023)

This Medical News article is an interview with Francis S. Collins, MD, PhD, former National Institutes of Health director, and JAMA Editor in Chief Kirsten Bibbins-Domingo, PhD, MD, MAS, about a historic Biden-Harris administration proposal to cure and prevent all hepatitis C infections in the US.
Burgos da Silva M, Ponce DM, Dai A, et al. Preservation of the fecal microbiome is associated with reduced severity of graft-versus-host disease. <i>Blood.</i> 2022;140(22):2385-2397.
Authors: Marina Burgos Da Silva, Doris Ponce, Anqi Dai, Sean Devlin, Antonio Gomes, Gillian Moore, John Slingerland, Roni Shouval, Gabriel Armijo, Susan Dewolf, Teng Fei, Annelie Clurman, Emily Fontana, Luigi Amoretti, Roberta Wright, Hana Andrlova, Oriana Miltiadous, Miguel-Angel Perales, Ying Taur, Jonathan Peled, Marcel Van Den Brink
Journal: Blood (2023)
<i>Erratum:</i> Vol. 72, No. 7
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

on page 181, the fifth sentence should have read, "By November-December 2022, 87% of U.S. children aged 6 months-4 years had evidence of infectioninduced SARS-CoV-2 immunity ¶ ¶ ¶ ¶ ¶ ; however, caregivers reported previous SARS-CoV-2 infection >3 months earlier for only approximately 20% of children in this analysis, and, therefore, the analysis was not adjusted for previous infection."
The Oncolytic Adenovirus XVir-N-31 Joins Forces with CDK4/6 Inhibition Augmenting Innate and Adaptive Antitumor Immunity in Ewing Sarcoma
Authors: Sebastian Johannes Schober, Caroline Schoening, Jennifer Eck, Charlotte Middendorf, Julia Lutsch, Pia Knoch, Anna Josefine von Ofen, Hendrik Gassmann, Melanie Thiede, Julia Hauer, Andreas Kolk, Klaus Mantwill, Jürgen E. Gschwend, Stefan E.G. Burdach, Roman Nawroth, Uwe Thiel, Per Sonne Holm
Journal: Clinical Cancer Research (2023)

Abstract Purpose: Ewing sarcoma (EwS) is a highly malignant pediatric tumor characterized by a non-T-cell-inflamed immune-evasive phenotype. When relapsed or metastasized, survival is poor, emphasizing the need for novel treatment strategies. Here, we analyze the novel combination approach using the YB-1-driven oncolytic adenovirus XVir-N-31 and CDK4/6 inhibition to augment EwS immunogenicity. Experimental Design: In vitro, viral toxicity, replication, and immunogenicity were studied in several EwS cell lines. In vivo tumor xenograft models with transient humanization were applied to evaluate tumor control, viral replication, immunogenicity, and dynamics of innate as well as human T cells after treatment with XVir-N-31 combined with CDK4/6 inhibition. Furthermore, immunologic features of dendritic cell maturation and T-cell-stimulating capacities were assessed. Results: The combination approach significantly increased viral replication and oncolysis in vitro, induced HLA-I upregulation, and IFNγ-induced protein 10 expression and enhanced maturation of monocytic dendritic cells with superior capacities to stimulate tumor antigen-specific T cells. These findings were confirmed in vivo showing tumor infiltration by (i) monocytes with antigen-presenting capacities and M1 macrophage marker genes, (ii) TReg suppression in spite of adenovirus infection, (iii) superior engraftment, and (iv) tumor infiltration by human T cells. Consequently, survival was improved over controls with signs of an abscopal effect after combination treatment. Conclusions: The joint forces of the YB-1-driven oncolytic adenovirus XVir-N-31 and CDK4/6 inhibition induce therapeutically relevant local and systemic antitumor effects. Innate as well as adaptive immunity against EwS is boosted in this preclinical setting, pointing toward high therapeutic potential in the clinic.
Daily point-of-care ultrasound-assessment of central venous catheter-related thrombosis in critically ill patients: a prospective multicenter study
Authors: Chunshuang Wu, Mao Zhang, Wenjie Gu, Caimu Wang, Xudong Zheng, Junfeng Zhang, Xingwen Zhang, Shijin Lv, Xuwei He, Xiaoyuan Shen, Wenlong Wei, Guotao Wang, Yingru Lu, Qingli Chen, Renfei Shan, Lingcong Wang, Feng Wu, Ting Shen, Xuebo Shao, Jiming Cai, Fuzheng Tao, Haiying Cai, Qin Lu, Chunshuang Wu, Mao Zhang, Wenjie Gu, Hong Liu, Qin Lu, Caimu Wang, Qijiang Chen, Weili Hong, Xudong Zheng, Junfeng Zhang, Zhiping Huang, Xingwen Zhang, Luping Wang, Shijin Lv, Dengpan Lai, Xuwei He, Ning Zhang, Qingli Chen, Xiaoyuan Shen, Lujiao Mo, Wenlong Wei, Yunchao Shi, Guotao Wang, Wansheng Li, Yingru Lu, Qin Chen, Renfei Shan, Jie Qin, Lingcong Wang, Chen Zhu, Feng Wu, Binbin Wu, Ting Shen, Lifeng Wu, Xuebo Shao, Weidong Tang, Qingyu Wang, Shaoyi Xu, Fuzheng Tao, Weiting Chen, Haiying Cai, Guojuan Ding, Tao Zhang, Qunjie Pan, Bei Tang, Jianbo Gao, Laifa Kong, Jinyan Fang, Junzhong Ke, Zhaohui Ji
Journal: Intensive Care Medicine (2023)
Incidence, aetiology and temporal trend of bloodstream infections in southern Sweden from 2006 to 2019: a population-based study
Authors: Oskar Ljungquist, Adam Blomstergren, Adam Merkel, Torgny Sunnerhagen, Karin Holm, Gustav Torisson
Journal: Eurosurveillance (2023)

BackgroundBloodstream infections (BSI) are a public health concern, and infections caused by resistant bacteria further increase the overall BSI burden on healthcare.AimTo provide a population-based estimate of BSI incidence and relate this to the forthcoming demographic ageing western population change.MethodsWe retrieved positive blood cultures taken from patients in the Skåne region, southern Sweden, 2006-2019 from the Clinical Microbiology Department database and estimated incidence rates (IR), stratified by age (0-49, 50-64, 65-79, ≥ 80 years), sex, year, and species and described antimicrobial susceptibility for Enterobacterales.ResultsWe identified 944,375 blood culture sets, and 129,274 (13.7%) were positive. After deduplication and removal of contaminants, 54,498 separate BSI episodes remained. In total, 30,003 BSI episodes (55%) occurred in men. The overall IR of BSI was 307/100,000 person-years, with an average annual increase of 3.0%. Persons ≥ 80 years had the highest IR, 1781/100,000 person-years, as well as the largest increase. Escherichia coli (27%) and Staphylococcus aureus (13%) were the most frequent findings. The proportion of Enterobacterales isolates resistant to fluoroquinolones and third generation cephalosporins increased from 8.4% to 13.6%, and 4.9% to 7.3%, (p for trend < 0.001), with the largest increase in the oldest age group.ConclusionWe report among the highest BSI IRs to date worldwide, with a higher proportion among elderly persons and males, including resistant isolates. Given expected demographic changes, these results indicate a possible substantial future BSI burden, for which preventive measures are needed.
Hepatitis B core-related antigen: A novel and promising surrogate biomarker to guide anti-hepatitis B virus therapy
Authors: Takako Inoue, Takehisa Watanabe, Yasuhito Tanaka
Journal: Clinical and Molecular Hepatology (2023)

The current requirement for biomarkers to detect hepatitis B virus (HBV) infection is polarized. One is a fully-automated and highly sensitive measurement system; the other is a simple system for point-of-care testing (POCT) in resource-limited areas. Hepatitis B core-related antigen (HBcrAg) reflects intrahepatic covalently closed circular DNA and serum HBV DNA. Even in patients with undetectable serum HBV DNA or HBsAg loss, HBcrAg may remain detectable. Decreased HBcrAg levels are associated with reduction of the occurrence of hepatocellular carcinoma (HCC) in chronic hepatitis B. Recently, a fully-automated, novel high-sensitivity HBcrAg assay (iTACT-HBcrAg, cut-off value: 2.1 logIU/mL) has been developed. This attractive assay has been released in Japan very recently. iTACT-HBcrAg can be useful for monitoring HBV reactivation and prediction of HCC occurrence, as an alternative to HBV DNA. Moreover, monitoring HBcrAg may be suitable for determining the therapeutic effectiveness of approved drugs and novel drugs under development. Presently, international guidelines recommend anti-HBV prophylaxis for pregnant women with high viral loads to prevent mother-to-child transmission of HBV. However, &gt;95% of HBV-infected individuals live in countries where HBV DNA quantification is not available. Worldwide elimination of HBV needs the scaling-up of examination and medication services in resource-limited areas. Based on this situation, a rapid and easy HBcrAg assay as a POCT is valuable. This review provides the latest information regarding the clinical use of a new surrogate marker, HBcrAg, in HBV management, based on iTACT-HBcrAg or POCT, and introduces novel agents targeting HBV RNA/protein.
Developing a Framework and Electronic Tool for Communicating Diagnostic Uncertainty in Primary Care
Authors: Maram Khazen, Maria Mirica, Narath Carlile, Alissa Groisser, Gordon D. Schiff
Journal: JAMA Network Open (2023)

Importance Communication of information has emerged as a critical component of diagnostic quality. Communication of diagnostic uncertainty represents a key but inadequately examined element of diagnosis. Objective To identify key elements facilitating understanding and managing diagnostic uncertainty, examine optimal ways to convey uncertainty to patients, and develop and test a novel tool to communicate diagnostic uncertainty in actual clinical encounters. Design, Setting, and Participants A 5-stage qualitative study was performed between July 2018 and April 2020, at an academic primary care clinic in Boston, Massachusetts, with a convenience sample of 24 primary care physicians (PCPs), 40 patients, and 5 informatics and quality/safety experts. First, a literature review and panel discussion with PCPs were conducted and 4 clinical vignettes of typical diagnostic uncertainty scenarios were developed. Second, these scenarios were tested during think-aloud simulated encounters with expert PCPs to iteratively draft a patient leaflet and a clinician guide. Third, the leaflet content was evaluated with 3 patient focus groups. Fourth, additional feedback was obtained from PCPs and informatics experts to iteratively redesign the leaflet content and workflow. Fifth, the refined leaflet was integrated into an electronic health record voice-enabled dictation template that was tested by 2 PCPs during 15 patient encounters for new diagnostic problems. Data were thematically analyzed using qualitative analysis software. Main Outcomes and Measures Perceptions and testing of content, feasibility, usability, and satisfaction with a prototype tool for communicating diagnostic uncertainty to patients. Results Overall, 69 participants were interviewed. A clinician guide and a diagnostic uncertainty communication tool were developed based on the PCP interviews and patient feedback. The optimal tool requirements included 6 key domains: most likely diagnosis, follow-up plan, test limitations, expected improvement, contact information, and space for patient input. Patient feedback on the leaflet was iteratively incorporated into 4 successive versions, culminating in a successfully piloted prototype tool as an end-of-visit voice recognition dictation template with high levels of patient satisfaction for 15 patients with whom the tool was tested. Conclusions and Relevance In this qualitative study, a diagnostic uncertainty communication tool was successfully designed and implemented during clinical encounters. The tool demonstrated good workflow integration and patient satisfaction.
Human mpox: Biology, epidemiology, therapeutic options, and development of small molecule inhibitors
Authors: Hairong Tang, Ao Zhang
Journal: Medicinal Research Reviews (2023)

Abstract Although monkeypox (mpox) has been endemic in Western and Central Africa for 50 years, it has not received sufficient prophylactic and therapeutical attention to avoid evolving into an epidemic. From January 2022 to January 2023, more than 84,000 of mpox cases were reported from 110 countries worldwide. Case numbers appear to be rising every day, making mpox an increasing global public health threat for the foreseeable future. In this perspective, we review the known biology and epidemiology of mpox virus, together with the latest therapeutic options available for mpox treatment. Further, small molecule inhibitors against mpox virus and the future directions in this field are discussed as well.
European Association of Urology-American Society of Clinical Oncology Collaborative Guideline on Penile Cancer: 2023 Update
Authors: Oscar R. Brouwer, Maarten Albersen, Arie Parnham, Chris Protzel, Curtis A. Pettaway, Benjamin Ayres, Tiago Antunes-Lopes, Lenka Barreto, Riccardo Campi, Juanita Crook, Sergio Fernández-Pello, Isabella Greco, Michiel S. van der Heijden, Peter A.S. Johnstone, Mithun Kailavasan, Kenneth Manzie, Jack David Marcus, Andrea Necchi, Pedro Oliveira, John Osborne, Lance C. Pagliaro, Herney A. Garcia-Perdomo, R. Bryan Rumble, Ashwin Sachdeva, Vasileios I. Sakalis, Łukasz Zapala, Diego F. Sánchez Martínez, Philippe E. Spiess, Scott T. Tagawa
Journal: European Urology (2023)
Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity
Authors: Benjamin Jaegle, Rahul Pisupati, Luz Mayela Soto-Jiménez, Robin Burns, Fernando A. Rabanal, Magnus Nordborg
Journal: Genome biology (2023)

Abstract Background It is apparent that genomes harbor much structural variation that is largely undetected for technical reasons. Such variation can cause artifacts when short-read sequencing data are mapped to a reference genome. Spurious SNPs may result from mapping of reads to unrecognized duplicated regions. Calling SNP using the raw reads of the 1001 Arabidopsis Genomes Project we identified 3.3 million (44%) heterozygous SNPs. Given that Arabidopsis thaliana ( A. thaliana ) is highly selfing, and that extensively heterozygous individuals have been removed, we hypothesize that these SNPs reflected cryptic copy number variation. Results The heterozygosity we observe consists of particular SNPs being heterozygous across individuals in a manner that strongly suggests it reflects shared segregating duplications rather than random tracts of residual heterozygosity due to occasional outcrossing. Focusing on such pseudo-heterozygosity in annotated genes, we use genome-wide association to map the position of the duplicates. We identify 2500 putatively duplicated genes and validate them using de novo genome assemblies from six lines. Specific examples included an annotated gene and nearby transposon that transpose together. We also demonstrate that cryptic structural variation produces highly inaccurate estimates of DNA methylation polymorphism. Conclusions Our study confirms that most heterozygous SNP calls in A. thaliana are artifacts and suggest that great caution is needed when analyzing SNP data from short-read sequencing. The finding that 10% of annotated genes exhibit copy-number variation, and the realization that neither gene- nor transposon-annotation necessarily tells us what is actually mobile in the genome suggests that future analyses based on independently assembled genomes will be very informative.
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
Authors: Marouen Ben Guebila, Tian Wang, Camila M. Lopes-Ramos, Viola Fanfani, Des Weighill, Rebekka Burkholz, Daniel Schlauch, Joseph N. Paulson, Michael Altenbuchinger, Katherine H. Shutta, Abhijeet R. Sonawane, James Lim, Genis Calderer, David G.P. van IJzendoorn, Daniel Morgan, Alessandro Marin, Cho-Yi Chen, Qi Song, Enakshi Saha, Dawn L. DeMeo, Megha Padi, John Platig, Marieke L. Kuijjer, Kimberly Glass, John Quackenbush
Journal: Genome biology (2023)

Abstract Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is a collection of open-source methods to infer GRNs, conduct differential network analyses, estimate community structure, and explore the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages and between methods to allow better integration of these tools into analytical pipelines. We demonstrate the utility using multi-omic data from the Cancer Cell Line Encyclopedia. We will continue to expand the netZoo to incorporate additional methods.